Merge branch 'singleplex-app' of https://github.com/vanvalenlab/deepc…

…ell-spots into singleplex-app
vanvalenlab · Jan 27, 2022 · 760e4ca · 760e4ca
2 parents 6c00c0a + 694262b
commit 760e4ca
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/deepcell_spots/applications/polaris.py b/deepcell_spots/applications/polaris.py
@@ -34,6 +34,7 @@
 import tensorflow as tf
 
 from deepcell.applications import CytoplasmSegmentation
+
 from deepcell_spots.applications import SpotDetection
 from deepcell_spots.singleplex import match_spots_to_cells
 from deepcell_toolbox.processing import histogram_normalization
@@ -87,9 +88,7 @@ def __init__(self,
     def predict(self,
                 image,
                 image_mpp=None,
-                # segmentation
                 cytoplasm_channel=0,
-                # spots
                 spots_channel=1,
                 threshold=0.95,
                 clip=False):
@@ -144,11 +143,11 @@ def predict(self,
 
         result = []
         for i in range(len(spots_result)):
-            spots_dict = match_spots_to_cells(segmentation_result[i:i + 1, :, :, :],
+            spots_dict = match_spots_to_cells(segmentation_result[i:i + 1],
                                               spots_result[i])
 
             result.append({'spots_assignment': spots_dict,
-                           'cell_segmentation': segmentation_result[i:i + 1, :, :, :],
+                           'cell_segmentation': segmentation_result[i:i + 1],
                            'spot_locations': spots_result[i]})
 
         return result
diff --git a/deepcell_spots/applications/spot_detection.py b/deepcell_spots/applications/spot_detection.py
@@ -232,7 +232,7 @@ def predict(self,
         """
 
         if threshold < 0 or threshold > 1:
-            raise ValueError("""Threshold value must be between 0 and 1.""")
+            raise ValueError('Threshold value must be between 0 and 1.')
 
         if preprocess_kwargs is None:
             preprocess_kwargs = {